Bioscience Evidence 2025, Vol.15, No.5, 237-248 http://bioscipublisher.com/index.php/be 239 3.2 Key genes: 3.2.1 Glyma. family genes regulating storage protein composition. Some Glyma.family genes (such as Glyma.20G088000, Glyma.16G066600, Glyma.19G185700, Glyma.19G186000) have been repeatedly discovered within the principal QTL interval. They are directly involved in the synthesis of glycoproteins and β -concombulins (Wang et al., 2021; Park et al., 2023; Zhang et al., 2024). In addition, some new candidate genes (such as Glyma.11g015500, Glyma.20g050300) have also been confirmed to be related to protein content through GWAS (Kim et al., 2023). 3.2.2 Transcription factors (e.g., bZIP, NAC, MYB) influencing protein accumulation Transcription factors are very important in the regulation of protein synthesis. Family members such as bZIP, NAC, and MYB can regulate storage protein genes, nitrogen metabolism, and seed enrichment, thereby affecting protein accumulation (Guo et al., 2022; Shen et al., 2022; Hooker et al., 2023; Tian et al., 2025). HSSP1 is a newly discovered regulatory factor. It can bind to the GmCG1 promoter, enhance its expression and increase seed protein. AIP2 affects the expression of glycoprotein and concombulinin genes by regulating the ABI3 transcription factor. 3.3 Functional mechanisms: carbon–nitrogen balance, seed filling, transcriptional regulation The accumulation of protein depends on the balance of carbon and nitrogen metabolism, amino acid synthesis and transport, as well as the distribution of substances during the seed enrichment stage. High-protein varieties usually have higher nitrogen utilization efficiency and stronger amino acid synthesis ability (Guo et al., 2022; Zhao et al., 2023; Zhang et al., 2024). Sugar transporters such as GmSWEET10a/b can affect carbon flow, thereby indirectly regulating protein and lipid accumulation (Wang et al., 2020). Furthermore, environmental factors, such as temperature and soil nitrogen, can also alter protein content by influencing gene expression (Hooker et al., 2023). 3.4 Breeding implications: challenges in raising protein without yield penalties Although the discovery of major QTLS and key genes provides targets for molecular marker selection (MAS) and gene editing, protein content is often negatively correlated with yield and oil content. When protein is increased, it is often accompanied by a decrease in yield (Patil et al., 2017; Zhang et al., 2019; Wang et al., 2021; Guo et al., 2022; Liu et al., 2023). However, some specific QTLS (such as Chr.20 QTL derived from Danbaekkong) can increase the protein in specific genetic contexts without significantly reducing the yield (Patil et al., 2017; Park et al., 2023). In the future, it is necessary to combine multi-gene aggregation, precise editing and excellent germplasm resources to break the contradiction between protein and yield and promote the breeding of high-protein and high-yield soybeans. 4 Genetic Basis of Oil Content 4.1 Major QTLs and loci: landmark discoveries from genetic studies Soybean seed oil content is a quantitative trait that is jointly controlled by many genes. Traditional linkage mapping and GWAS have identified hundreds of related QTLS on 20 chromosomes. Some QTLS on Chr.5, Chr.10, Chr.14 and Chr.20 (such as qOil-5-1, qOil-10-1, qOil-14-1, GqOil20) are very stable in different populations and environments. It can explain up to 26.3% of the phenotypic differences (Cao et al., 2017; Zhang et al., 2019; Jia et al., 2024). Meta-QTL and multi-omics analyses further narrowed the candidate regions and enhanced the value of breeding utilization (Jia et al., 2024; Yuan et al., 2024; Zhao et al., 2024). 4.2 Key genes 4.2.1 DGAT1 (diacylglycerol acyltransferase 1), WRI1, OLE1 regulators DGAT1 is the rate-limiting enzyme for triacylglycerol (TAG) synthesis, and overexpression can significantly increase seed oil content (Zhao et al., 2024). WRI1 is a core transcription factor that can regulate genes related to glycolysis and fatty acid synthesis and promote lipid accumulation. GmOLEO1 encodes the structural proteins of oil bodies and affects the formation and stability of oil bodies. Its overexpression can increase oil content by more than 10% and was strongly selected during domestication (Zhang et al., 2019).
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